samples:
own: 1011GI.vcf.gz
ref: 1KGP.vcf.gz
population_file: Pop.csv
chromosome: 2
threads: 72
Analysis:
ADMIXTURE: False
SmartPCA: False
iHS: False
XPEHH: False
TreeMIX: False
QualityCheck:
own:
geno: 0.02
mind: False
maf: 0.001
hwe: 1e-6
heterozygosity:
StandardDeviations: 3
LDPruning:
WindowSize: 1000
Shift: 10
CorrelationCoefficient: 0.15
ref:
geno: 0.02
mind: False
maf: 0.001
hwe: 1e-6
heterozygosity:
StandardDeviations: False
LDPruning:
WindowSize: 1000
Shift: 10
CorrelationCoefficient: 0.15
iHS:
maf: 0.05
bins: 40
pop: ['Adikarnataka' , 'Iyengar' , 'Kolis' , 'Lingayath' , 'Marathas' , 'Deshastha_Brhamin' , 'Konkanastha_brahmin', 'Nadar' , 'Naidu' , 'Namboodari' , 'Parayan' , 'Vakkaliga' , 'Vidiki_Brhamin']
pop_type: Pop
xpEHH:
pop: ['OWN']
reference_pop: ['AFR' , 'AMR' , 'EAS' , 'EUR' , 'SAS']
pop_type: SuperPop
mapping_pop: ['OWN']
bins: 100
ADMIXTURE:
K: 2
iterations: 1
LDPruning:
WindowSize: 1000
Shift: 10
CorrelationCoefficient: 0.15
SmartPCA:
LDPruning:
WindowSize: 1000
Shift: 10
CorrelationCoefficient: 0.15
Ethnicity_pop: ['OWN']
pop_type: SuperPop
TreeMIX:
Root: YRI
MigrationEdges: 1
LDPruning:
WindowSize: 1000
Shift: 10
CorrelationCoefficient: 0.15